This is (for example) because the node-type form sets the variable "updown_comment_votedown_$type" but the code that creates the output is looking for updown_unvote_comment_$type (ie: wrong order).
// create the output
$widget = (user_access('rate content with updown')) ? theme('updown_active_widget', 'comment', $comment->cid, variable_get('updown_unvote_comment_'. $node->type, FALSE), variable_get('updown_votedown_comment_'. $node->type, TRUE)) : theme('updown_inactive_widget', 'comment', $comment->cid);
// settings page
$form['updown_comment']['updown_comment_votedown'] = array(
'#type' => 'checkbox',
'#title' => t('Allow users to vote content down'),
'#default_value' => variable_get('updown_comment_votedown_'. $form['#node_type']->type, 1),
'#return_value' => 1,
);